Contacts of the helix formed by residues 159 - 176 (chain B) in PDB entry 3S9L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B PRO* 3.9 9.0 + - - -
156B GLU* 2.7 29.7 + - - -
157B ALA 3.3 0.8 + - - -
158B GLY* 1.3 82.0 - - - +
160B GLN* 1.3 59.7 + - - +
161B LYS* 3.5 9.0 + - - +
162B ASP* 2.8 25.0 + - - +
163B GLU* 2.9 28.7 + - - +
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY 4.1 0.2 + - - -
159B SER* 1.3 75.1 - - - +
161B LYS* 1.3 53.6 + - - +
163B GLU* 3.8 20.8 + - - +
164B ASN* 2.6 55.9 + - - +
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Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER 3.6 18.2 - - - +
152B TYR* 4.2 7.9 - - - -
154B PRO* 2.9 36.8 - - + +
155B ARG* 5.5 0.7 - - - -
159B SER* 3.1 3.3 - - - +
160B GLN* 1.3 79.2 - - - +
162B ASP* 1.3 63.8 + - - +
164B ASN* 3.0 22.0 + - - +
165B LEU* 3.2 13.3 + - - +
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Residues in contact with ASP 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B PRO 4.2 0.6 + - - -
155B ARG* 3.9 14.6 - - - +
156B GLU 3.3 7.2 - - - +
157B ALA* 3.0 11.7 - - - -
158B GLY* 2.9 22.2 + - - -
159B SER* 2.8 26.5 + - - +
161B LYS* 1.3 79.1 - - - +
163B GLU* 1.3 60.8 + - - +
165B LEU* 3.4 5.1 + - - +
166B ALA 3.3 14.0 + - - -
409B ARG* 2.6 41.7 + - - +
410B ASP* 4.0 7.4 - - - +
454B SER* 3.2 11.6 + - - -
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY 5.1 4.4 - - - +
159B SER 2.9 17.8 + - - +
160B GLN* 3.8 24.9 + - - +
162B ASP* 1.3 77.7 + - - +
164B ASN* 1.3 55.2 + - - +
166B ALA* 3.0 16.4 - - - +
167B LEU* 2.8 43.4 - - + +
385B LYS* 4.8 19.1 + - - +
387B LEU* 4.7 26.7 - - + +
409B ARG* 5.1 0.7 - - - +
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Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B SER* 4.6 6.5 - - - +
152B TYR* 4.4 12.9 + - + -
160B GLN* 2.6 47.8 + - - +
161B LYS* 3.0 14.0 + - - +
163B GLU* 1.3 73.9 - - - +
165B LEU* 1.3 66.6 + - - +
166B ALA 3.2 0.3 + - - -
167B LEU* 3.3 13.0 + - - +
168B TYR* 3.1 19.4 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LEU* 3.7 22.7 - - + -
152B TYR* 3.9 22.8 - - + -
155B ARG* 2.9 47.1 - - - +
161B LYS 3.2 6.2 + - - +
162B ASP* 3.7 9.9 - - - +
164B ASN* 1.3 76.9 - - - +
166B ALA* 1.3 69.2 + - - +
168B TYR* 3.2 28.0 + - + +
169B VAL* 3.0 31.4 + - + +
409B ARG* 3.3 19.5 - - + +
423B THR* 4.8 4.7 - - + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ASP 3.3 5.9 + - - +
163B GLU* 3.0 22.9 + - - +
165B LEU* 1.3 78.7 - - - +
167B LEU* 1.3 68.1 + - + +
169B VAL* 3.0 15.3 + - - +
170B GLU* 3.1 12.8 + - - +
387B LEU* 4.4 10.1 - - + -
389B ILE* 3.9 26.1 - - + +
409B ARG* 3.7 19.9 - - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLU* 2.8 44.4 + - + +
164B ASN* 3.3 11.9 + - - +
166B ALA* 1.3 81.4 - - + +
168B TYR* 1.3 56.5 + - - +
170B GLU* 3.8 14.2 - - - +
171B ASN* 2.8 34.4 + - - +
387B LEU* 5.1 6.1 - - + -
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B THR* 5.8 3.6 - - + +
146B LEU* 4.0 29.2 - - + +
147B LEU* 4.2 17.7 - - + -
152B TYR* 4.1 13.5 - - - +
164B ASN 3.1 12.6 + - - +
165B LEU* 3.3 31.6 - - + +
166B ALA 3.0 0.6 + - - -
167B LEU* 1.3 78.0 - - - +
169B VAL* 1.3 55.3 + - + +
171B ASN* 3.7 3.7 - - + +
172B GLN* 2.8 62.6 + - + +
427B LEU* 4.3 16.3 - - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 3.0 26.4 + - + +
166B ALA 3.0 5.3 + - - +
168B TYR* 1.3 78.0 - - + +
170B GLU* 1.3 53.0 + - - +
172B GLN* 2.9 8.9 + - - +
173B PHE* 2.8 67.4 + - + -
389B ILE* 4.1 8.7 - - + -
409B ARG* 4.1 16.8 - - - -
423B THR* 4.5 11.4 - - + -
426B LEU* 4.9 3.4 - - + -
427B LEU* 4.2 12.6 - - + -
452B SER* 4.4 13.7 - - - +
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA 3.1 11.3 + - - +
167B LEU* 3.8 12.6 - - - +
169B VAL* 1.3 79.9 - - - +
171B ASN* 1.3 61.8 + - - +
173B PHE* 3.7 4.3 + - - +
174B ARG* 3.2 38.6 + - - +
181B VAL* 4.0 19.3 - - + +
182B TRP* 5.6 0.9 - - - +
183B ARG* 3.4 28.9 - - + +
387B LEU* 5.5 2.9 - - - +
389B ILE* 3.6 25.1 - - + +
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LEU 2.8 19.5 + - - +
168B TYR* 3.8 5.2 - - + +
170B GLU* 1.3 75.2 - - - +
172B GLN* 1.3 60.5 + - - +
174B ARG* 3.5 17.7 + - - +
175B GLU* 3.0 26.9 + - - +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 2.8 45.4 + - + +
169B VAL* 3.2 4.9 - - - +
171B ASN* 1.3 76.1 - - - +
173B PHE* 1.3 59.9 + - - +
175B GLU* 3.1 15.8 + - - +
176B PHE* 3.0 78.4 + - + -
427B LEU* 3.4 19.5 - - + -
431B GLN* 5.9 0.2 - - - -
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 2.8 45.9 + - + +
170B GLU* 3.8 5.4 - - - +
172B GLN* 1.3 68.7 - - - +
174B ARG* 1.3 65.8 + - - +
176B PHE* 2.9 35.4 + + - +
177B LYS 3.3 4.2 + - - -
178B LEU* 3.5 30.4 + - + +
181B VAL* 4.1 9.9 - - + -
389B ILE* 3.6 24.5 - - + -
390B PHE 4.2 1.3 - - - -
391B GLY* 4.1 17.0 - - - -
426B LEU* 4.2 17.7 - - + -
427B LEU* 4.5 5.8 - - + -
430B ALA* 3.6 22.0 - - + -
450B PHE* 3.9 23.3 - - + -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLU* 3.2 36.6 + - - +
171B ASN* 3.6 18.9 - - - +
173B PHE* 1.3 78.5 - - - +
175B GLU* 1.3 57.9 + - - +
177B LYS* 2.9 21.6 + - - +
178B LEU 5.1 0.9 - - - +
181B VAL* 4.2 25.2 + - + +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ASN* 3.0 18.2 + - - +
172B GLN* 3.2 24.5 - - - +
173B PHE 3.1 0.2 - - - -
174B ARG* 1.3 72.6 - - - +
176B PHE* 1.3 58.7 + - + +
177B LYS* 2.9 14.1 + - - +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B GLN* 3.0 62.4 + - + -
173B PHE* 2.9 33.7 + + - +
175B GLU* 1.3 76.0 - - + +
177B LYS* 1.3 63.0 + - - +
178B LEU* 4.1 5.2 - - + -
427B LEU* 3.8 28.9 - - + -
430B ALA* 4.1 8.5 - - + -
431B GLN* 3.6 38.1 - - + -
434B SER* 2.6 37.2 + - - +
435B ASP* 5.5 1.7 - - - +
438B LEU* 5.9 0.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il